Got the email for this thread today, and it caught my eye so I've read through it. I might have another answer for you guys as to why manual cars in particular do this, and I'm pretty sure it has little to do with the ECU.
First, some details on my own car; it's a 2009 Mazdaspeed 3 with factory drive by wire and electronic throttle body.
Now, for some anecdotal information:
A few years ago, I was redoing the PCV setup on my car to help with oil going all over the place in the intake and whatnot, and I completely bypassed (capped) the line going into the intake manifold (post throttle body). It ran fine except under one condition: Holding the clutch in after hitting high RPMs and letting the car coast.
With no air bypassing the throttle body (via PCV), RPMs would drop sub-idle and usually stall. Sometimes it would hunt for idle RPM a few times, but normally it would stall out. I fixed this issue by installing a hose to the intake manifold with a low spring check valve that goes to the intake, post MAF (so it doesn't pull in unmetered air).
My thought is that there's still some coupling going on which is causing the engine RPMs to run higher than idle (similar to how a manual car in neutral on jackstands will have the drive wheels turn slowly).
I vaguely recall seeing the throttle body reading the same as idle or below idle settings when I was troubleshooting this issue myself, but I've asked a friend to pull some logged data for me to confirm since my car is down. I should have the data within a couple of hours of the time of this post.
Stay tuned!
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